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Human activity has increased loading of reactive nitrogen (N) in the environment, with important and often deleterious impacts on biodiversity, climate, and human health. Since the fate of N in the ecosystem is mainly controlled by microorganisms, understanding the factors that shape microbial communities becomes relevant and urgent. In arid land soils, these microbial communities and factors are not well understood. I aimed to study the role of N cycling microbes, such as the ammonia-oxidizing bacteria (AOB), the recently discovered ammonia-oxidizing archaea (AOA), and various fungal groups, in soils of arid lands. I also tested if niche differentiation among microbial populations is a driver of differential biogeochemical outcomes. I found that N cycling microbial communities in arid lands are structured by environmental factors to a stronger degree than what is generally observed in mesic systems. For example, in biological soil crusts, temperature selected for AOA in warmer deserts and for AOB in colder deserts. Land-use change also affects niche differentiation, with fungi being the major agents of N2O production in natural arid lands, whereas emissions could be attributed to bacteria in mesic urban lawns. By contrast, NO3- production in the native desert and managed soils was mainly controlled by autotrophic microbes (i.e., AOB and AOA) rather than by heterotrophic fungi. I could also determine that AOA surprisingly responded positively to inorganic N availability in both short (one month) and long-term (seven years) experimental manipulations in an arid land soil, while environmental N enrichment in other ecosystem types is known to favor AOB over AOA. This work improves our predictions of ecosystem response to anthropogenic N increase and shows that paradigms derived from mesic systems are not always applicable to arid lands. My dissertation also highlights the unique ecology of ammonia oxidizers and draws attention to the importance of N cycling in desert soils.
ContributorsMarusenko, Yevgeniy (Author) / Hall, Sharon J (Thesis advisor) / Garcia-Pichel, Ferran (Thesis advisor) / Mclain, Jean E (Committee member) / Schwartz, Egbert (Committee member) / Arizona State University (Publisher)
Created2013
Description
Sexually transmitted diseases like gonorrhea and chlamydia, standardly treated with antibiotics, produce over 1.2 million cases annually in the emergency department (Jenkins et al., 2013). To determine a need for antibiotics, hospital labs utilize bacterial cultures to isolate and identify possible pathogens. Unfortunately, this technique can take up to 72 hours, leading to several physicians presumptively treating patients based solely on history and physical presentation. With vague standards for diagnosis and a high percentage of asymptomatic carriers, several patients undergo two scenarios; over- or under-treatment. These two scenarios can lead to consequences like unnecessary exposure to antibiotics and development of secondary conditions (for example: pelvic inflammatory disease, infertility, etc.). This presents a need for a laboratory technique that can provide reliable results in an efficient matter. The viability of DNA-based chip targeted for C. trachomatis, N. gonorrhoeae, and other pathogens of interest were evaluated. The DNA-based chip presented several advantages as it can be easily integrated as a routine test given the process is already well-known, is customizable and able to target multiple pathogens within a single test and has the potential to return results within a few hours as opposed to days. As such, implementation of a DNA-based chip as a diagnostic tool is a timely and potentially impactful investigation.
ContributorsCharoenmins, Patherica (Author) / Penton, Christopher (Thesis director) / Moore, Marianne (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
There is a growing consensus that photodegradation accelerates litter decomposition in drylands, but the mechanisms are not well understood. In a previous field study examining how exposure to solar radiation affects decomposition of 12 leaf litter types over 34 months in the Sonoran Desert, litter exposed to UV/blue wavebands of solar radiation decayed faster. The concentration of water-soluble compounds was higher in decayed litter than in new (recently senesced) litter, and higher in decayed litter exposed to solar radiation than other decayed litter. Microbial respiration of litter incubated in high relative humidity for 1 day was greater in decayed litter than new litter and greatest in decayed litter exposed to solar radiation. Respiration rates were strongly correlated with decay rates and water-soluble concentrations of litter. The objective of the current study was to determine why respiration rates were higher in decayed litter and why this effect was magnified in litter exposed to solar radiation. First, I evaluated whether photodegradation enhanced the quantity of dissolved organic carbon (DOC) in litter by comparing DOC concentrations of photodegraded litter to new litter. Second, I evaluated whether photodegradation increased the quality of DOC for microbial utilization by measuring respiration of leachates with equal DOC concentrations after applying them to a soil inoculum. I hypothesized that water vapor sorption may explain differences in respiration among litter age or sunlight exposure treatments. Therefore, I assessed water vapor sorption of litter over an 8-day incubation in high relative humidity. Water vapor sorption rates over 1 and 8 days were slower in decayed than new litter and not faster in photodegraded than other decayed litter. However, I found that 49-78% of the variation in respiration could be explained by the relative amount of water litter absorbed over 1 day compared to 8 days, a measure referred to as relative water content. Decayed and photodegraded litter had higher relative water content after 1 day because it had a lower water-holding capacity. Higher respiration rates of decayed and photodegraded litter were attributed to faster microbial activation due to greater relative water content of that litter.
ContributorsBliss, Michael Scott (Author) / Day, Thomas A. (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Throop, Heather L. (Committee member) / Arizona State University (Publisher)
Created2019
Description
Desert organisms lead harsh lives owing to the extreme, often unpredictable environmental conditions they endure. Climate change will likely make their existence even harsher. Predicting the ecological consequences of future climate scenarios thus requires understanding how the biota will be affected by climatic shifts. Biological soil crusts (biocrusts) are an important ecosystem component in arid lands, one that covers large portions of the landscape, improving soil stability and fertility. Because cyanobacteria are biocrust’s preeminent primary producers, eking out an existence during short pulses of precipitation, they represent a relevant global change object of study. I assessed how climate scenarios predicted for the Southwestern United States (US) will affect biocrusts using long-term, rainfall-modifying experimental set-ups that imposed either more intense drought, a seasonally delayed monsoon season, or a shift to smaller but more frequent precipitation events. I expected drought to be detrimental, but not a delay in the monsoon season. Surprisingly, both treatments showed similar effects on cyanobacterial community composition and population size after four years. While successionally incipient biocrusts were unaffected, mature biocrusts lost biomass and diversity with treatment, especially among nitrogen-fixing cyanobacteria. In separate experiments, I assessed the effect of rainfall with modified event size and frequency after a decade of treatment. Small, frequent rainfall events surprisingly enhanced the diversity and biomass of bacteria and cyanobacteria, with clear winners and losers: nitrogen-fixing Scytonema sp. benefited, while Microcoleus vaginatus lost its dominance. As an additional finding, I could also show that water addition is not always beneficial to biocrusts, calling into question the notion that these are strictly water-limited systems.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
Finally, results interpretation was severely hampered by a lack of appropriate systematic treatment for an important group of biocrust cyanobacteria, the “Microcoleus steenstrupii complex”. I characterized the complex using a polyphasic approach, leading to the formal description of a new family (Porphyrosiphonaceae) of desiccation resistant cyanobacteria that includes 11 genera, of which 5 had to be newly described. Under the new framework, the distribution and abundance of biocrust cyanobacteria with respect to environmental conditions can now be understood. This body of work contributes significantly to explain current distributional patterns of biocrust cyanobacteria and to predict their fate in the face of climate change.
ContributorsMoreira Camara Fernandes, Vanessa (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Rudgers, Jennifer (Committee member) / Sala, Osvaldo (Committee member) / Penton, Christopher (Committee member) / Arizona State University (Publisher)
Created2020
Description
Biological soil crusts (BSCs) dominate the soil surface of drylands in the western United States and possess properties thought to influence local hydrology. Little agreement exists, however, on the effects of BSCs on runoff, infiltration, and evaporative rates. This study aims to improve the predictive capability of an ecohydrology model in order to understand how BSCs affect the storage, retention, and infiltration of water into soils characteristic of the Colorado Plateau. A set of soil moisture measurements obtained at a climate manipulation experiment near Moab, Utah, are used for model development and testing. Over five years, different rainfall treatments over experimental plots resulted in the development of BSC cover with different properties that influence soil moisture differently. This study used numerical simulations to isolate the relative roles of different BSC properties on the hydrologic response at the plot-scale. On-site meteorological, soil texture and vegetation property datasets are utilized as inputs into a ecohydrology model, modified to include local processes: (1) temperature-dependent precipitation partitioning, snow accumulation and melt, (2) seasonally-variable potential evapotranspiration, (3) plant species-specific transpiration factors, and (4) a new module to account for the water balance of the BSC. Soil, BSC and vegetation parameters were determined from field measurements or through model calibration to the soil moisture observations using the Shuffled Complex Evolution algorithm. Model performance is assessed against five years of soil moisture measurements at each experimental site, representing a wide range of crust cover properties. Simulation experiments were then carried out using the calibrated ecohydrology model in which BSC parameters were varied according to the level of development of the BSC, as represented by the BSC roughness. These results indicate that BSCs act to both buffer against evaporative soil moisture losses by enhancing BSC moisture evaporation and significantly alter the rates of soil water infiltration by reducing moisture storage and increasing conductivity in the BSC. The simulation results for soil water infiltration, storage and retention across a wide range of meteorological events help explain the conflicting hydrologic outcomes present in the literature on BSCs. In addition, identifying how BSCs mediate infiltration and evaporation processes has implications for dryland ecosystem function in the western United States.
ContributorsWhitney, Kristen M (Author) / Vivoni, Enrique R (Thesis advisor) / Farmer, Jack D (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2015
Description
Decay of plant litter represents an enormous pathway for carbon (C) into the atmosphere but our understanding of the mechanisms driving this process is particularly limited in drylands. While microbes are a dominant driver of litter decay in most ecosystems, their significance in drylands is not well understood and abiotic drivers such as photodegradation are commonly perceived to be more important. I assessed the significance of microbes to the decay of plant litter in the Sonoran Desert. I found that the variation in decay among 16 leaf litter types was correlated with microbial respiration rates (i.e. CO2 emission) from litter, and rates were strongly correlated with water-vapor sorption rates of litter. Water-vapor sorption during high-humidity periods activates microbes and subsequent respiration appears to be a significant decay mechanism. I also found that exposure to sunlight accelerated litter decay (i.e. photodegradation) and enhanced subsequent respiration rates of litter. The abundance of bacteria (but not fungi) on the surface of litter exposed to sunlight was strongly correlated with respiration rates, as well as litter decay, implying that exposure to sunlight facilitated activity of surface bacteria which were responsible for faster decay. I also assessed the response of respiration to temperature and moisture content (MC) of litter, as well as the relationship between relative humidity and MC. There was a peak in respiration rates between 35-40oC, and, unexpectedly, rates increased from 55 to 70oC with the highest peak at 70oC, suggesting the presence of thermophilic microbes or heat-tolerant enzymes. Respiration rates increased exponentially with MC, and MC was strongly correlated with relative humidity. I used these relationships, along with litter microclimate and C loss data to estimate the contribution of this pathway to litter C loss over 34 months. Respiration was responsible for 24% of the total C lost from litter – this represents a substantial pathway for C loss, over twice as large as the combination of thermal and photochemical abiotic emission. My findings elucidate two mechanisms that explain why microbial drivers were more significant than commonly assumed: activation of microbes via water-vapor sorption and high respiration rates at high temperatures.
ContributorsTomes, Alexander (Author) / Day, Thomas (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Ball, Becky (Committee member) / Hall, Sharon (Committee member) / Roberson, Robert (Committee member) / Arizona State University (Publisher)
Created2020